Rapid sympatric ecological differentiation of crater lake cichlid fishes within historic times

Background: After a volcano erupts, a lake may form in the cooled crater and become an isolated aquatic ecosystem. This makes fishes in crater lakes informative for understanding sympatric evolution and ecological diversification in barren environments. From a geological and limnological perspective, such research offers insight about the process of crater lake ecosystem establishment and speciation. In the present study we use genetic and coalescence approaches to infer the colonization history of Midas cichlid fishes (Amphilophus cf. citrinellus) that inhabit a very young crater lake in Nicaragua-the ca. 1800 year-old Lake Apoyeque. This lake holds two sympatric, endemic morphs of Midas cichlid: one with large, hypertrophied lips (~20% of the total population) and another with thin lips. Here we test the associated ecological, morphological and genetic diversification of these two morphs and their potential to represent incipient speciation.
Results: Gene coalescence analyses [11 microsatellite loci and mitochondrial DNA (mtDNA) sequences] suggest that crater lake Apoyeque was colonized in a single event from the large neighbouring great lake Managua only about 100 years ago. This founding in historic times is also reflected in the extremely low nuclear and mitochondrial genetic diversity in Apoyeque. We found that sympatric adult thin- and thick-lipped fishes occupy distinct ecological trophic niches. Diet, body shape, head width, pharyngeal jaw size and shape and stable isotope values all differ significantly between the two lip-morphs. The eco-morphological features pharyngeal jaw shape, body shape, stomach contents and stable isotopes (d15N) all show a bimodal distribution of traits, which is compatible with the expectations of an initial stage of ecological speciation under disruptive selection. Genetic differentiation between the thin- and thick-lipped population is weak at mtDNA sequence (FST = 0.018) and absent at nuclear microsatellite loci (FST < 0.001).
Conclusions: This study provides empirical evidence of eco-morphological differentiation occurring very quickly after the colonization of a new and vacant habitat. Exceptionally low levels of neutral genetic diversity and inference from coalescence indicates that the Midas cichlid population in Apoyeque is much younger (ca. 100 years or generations old) than the crater itself (ca. 1 800 years old). This suggests either that the crater remained empty for many hundreds of years after its formation or that remnant volcanic activity prevented the establishment of a stable fish population during the early life of the crater lake. Based on our findings of eco-morphological variation in the Apoyeque Midas cichlids, and known patterns of adaptation in Midas cichlids in general, we suggest that this population may be in a very early stage of speciation (incipient species), promoted by disruptive selection and ecological diversification.

Both English and Latin: Bilingualism and Biculturalism in Milton's Neo-Latin Writings (219pp.)

Review by Emma A. Wilson, Milton Quarterly 49.1 (March, 2015), 54-59:

‘This volume provides an invaluable new perspective on both Milton’s neo-Latin poems and also the major vernacular poetry by insisting politely but firmly upon the bilingualism of their author and the manifest effects of that bilingualism upon style and intertextuality in his corpus. Through a dextrous combination of manuscript research, modern understandings of bilingualism, and crucially meticulous and demanding close readings, this volume succeeds in vivifying a wealth of new relationships between Milton’s neo-Latin works and his vernacular poems … Haan is expert in probing and elucidating the multiple linguistic and cultural lenses through which Milton projects his work, and the resulting volume brings a new set of historical contexts and consequences for both the major and minor texts, whilst also more importantly furnishing an exciting new method with which to approach these works as a whole ... Haan's linguistic expertise and meticulous archival research combine to create a critical work in which discoveries gradually accumulate and speak to one another in very specific, nuanced dialogues between chapters ... opening up exciting new reading vistas ... The final two chapters, in which Haan harvests some of the fruits of her considerable and fantastic labor in the archives and in current linguistic research into bilingualism, bring to light fresh perspectives on some of Milton's major published poetic works.’


Both English and Latin: Bilingualism and Biculturalism in Milton’s Neo-Latin Writings (2012) (Back Cover):

Gordon Campbell, University of Leicester:
‘Estelle Haan is the world’s foremost authority on Milton’s Latin poetry, and probably the most distinguished student of that poetry in the history of critical commentary. This is a work of extraordinary authority written by a scholar at the height of her powers. In short, this is a terrific book, elegant and informative.’

Anne Mahoney, Tufts University:
‘This book ssucceeds in presenting Milton's poetry as a single, unified body of work. Its biggest strength is the many close readings of Milton's Latin verse as engagements with classical Latin literature. In addition to introducing the Latin verse to new readers, it provides a new approach to Paradise Lost, one that accounts for one of the difficulties of Milton’s text—its language—in a novel way.’


Abstract:

Both English and Latin examines the interplay of Latin and English in a selection of John Milton's neo-Latin writings. It argues that this interplay is indicative of an inherent bilingualism that proceeds hand-in-hand with a self-fashioning that is bicultural in essence. Interlingual flexibility ultimately proved central to the poet of Paradise Lost, an epic uniquely characterized by its Latinate vernacular and its vernacular Latinitas.

Male morph predicts investment in larval immune function in the dung beetle, Onthophagus taurus

Investment in immunity is costly, so that resource-based trade-offs between immunity and sexually selected ornaments might be expected. The amount of resources that an individual can invest in each trait will be limited by the total resources available to them. It would therefore be informative to investigate how investment in immune function changes during growth or production of the sexual trait as resources are diverted to it. Using the dung beetle, Onthophagus taurus, which displays both sexual and male dimorphism in horn size, we examined changes in one measure of immune function, phenoloxidase (PO) activity, in the hemolymph of larvae prior to and during horn growth. We found that PO levels differed between small- and large-horned males throughout the final instar prior to the point where investment in horn growth was taking place. PO levels in females were intermediate to the 2 male morphs. These differences could not be accounted for by differences in condition, measured as hemolymph protein levels and weight. We suggest that the observed differences might be associated with sex- and morph-specific variation in juvenile hormone levels.

Intertidal molluscan and algal species richness around the UK coast

Geographically referenced databases of species records are becoming increasingly available. Doubts over the heterogeneous quality of the underlying data may restrict analyses of such collated databases. We partitioned the spatial variation in species richness of littoral algae and molluscs from the UK National Biodiversity Network database into a smoothed mesoscale component and a local component. Trend surface analysis (TSA) was used to define the mesoscale patterns of species richness, leaving a local residual component that lacked spatial autocorrelation. The analysis was based on 10 km grid squares with 115035 records of littoral algae (729 species) and 66879 records of littoral molluscs (569 species). The TSA identified variation in algal and molluscan species richness with a characteristic length scale of approximately 120 km. Locations of the most species-rich grid squares were consistent with the southern and western bias of species richness in the UK marine flora and fauna. The TSA also identified areas which showed significant changes in the spatial pattern of species richness: breakpoints, which correspond to major headlands along the south coast of England. Patterns of algal and molluscan species richness were broadly congruent. Residual variability was strongly influenced by proxies of collection effort, but local environmental variables including length of the coastline and variability in wave exposure were also important. Relative to the underlying trend, local species richness hotspots occurred on all coasts. While there is some justification for scepticism in analyses of heterogeneous datasets, our results indicate that the analysis of collated datasets can be informative.

Genetic diversity of liver flukes (Fasciola hepatica) from Eastern Europe.

The genetic diversity of liver fluke populations in three different countries from Eastern Europe (Greece, Bulgaria, and Poland) in comparison with available data from other countries was determined. Specifically, SNPs from regions of two nuclear genes, 28S rDNA, ß-tubulin 3 and an informative region of the mitochondrial genome were examined. Two major lineages for the 28S rDNA gene based on the highly polymorphic 105th nucleotide position were found. These lineages were widely and almost equally spread not only through the countries studied but also in other investigated geographical areas. Two basic lineages and additional haplotypes were defined for the mtDNA gene region, consisting of the cytochrome c oxidase subunit III gene, transfer RNA histidine gene and cytochome b gene. The basic lineages were observed within Greek, Bulgarian, and Polish Fasciola hepatica populations but the distribution of additional haplotypes differed between the populations from the three countries. For the ß-tubulin 3 gene multiple polymorphic sites were revealed but no explicit clades. The SNPs were spread unequally in all studied geographical regions with an evident distinction between the Greek and Polish specimens. Additional genotypes for the 28S rDNA region as well as haplotypes of the mtDNA region that were typical for the Greek or Polish populations were observed. Significant polymorphisms for ß-tubulin 3 gene were displayed with decreasing percentage of presence within populations from Greece to Poland. There was an amino acid substitution in ß-tubulin 3 protein found only among Polish specimens. It is hypothesized that genotypic differences between Greek, Bulgarian, and Polish liver fluke populations are due to territorial division and genetic drift in past epochs.

Accuracy of Death Certificates in COPD: Analysis from the TORCH Trial

The Towards a Revolution in COPD Health (TORCH) trial was an international clinical trial of chronic obstructive pulmonary disease (COPD) patients where cause of death was assigned by an independent committee. Comparison of death certificate data and adjudicated cause of death allows a unique opportunity to determine death certificate accuracy and frequency of COPD listing on death certificates of COPD patients. In this analysis, the authors determine the concordance between adjudicated cause of death and primary and secondary cause of death from death certificates. In 317 (80%) of informative deaths, the primary or secondary cause of death from certificates agreed with adjudicated cause of death. Only 229 (58%) of death certificates in these COPD patients listed COPD on the certificate. COPD was not listed on the death certificate in 21% of deaths adjudicated to be caused by COPD exacerbation. Compared with pulmonary causes, the listing of COPD on certificates occurred with less frequency than cardiovascular, cancer and other categories of death. The combined primary and secondary listing on death certificates has good concordance with actual cause of death. COPD is under-reported on death certificates, and this under-reporting is more frequent when the primary cause of death is not pulmonary.

Decreased respiratory system compliance on the sixth day of mechanical ventilation is a predictor of death in patients with established acute lung injury

Background: Multiple studies have identified single variables or composite scores that help risk stratify patients at the time of acute lung injury (ALI) diagnosis. However, few studies have addressed the important question of how changes in pulmonary physiologic variables might predict mortality in patients during the subacute or chronic phases of ALI. We studied pulmonary physiologic variables, including respiratory system compliance, P/F ratio and oxygenation index, in a cohort of patients with ALI who survived more than 6 days of mechanical ventilation to see if changes in these variables were predictive of death and whether they are informative about the pathophysiology of subacute ALI.

Verwirklichende Raume - Poetik und Raumkonzeption bei Paul Celan und Martin Buber

This article with the conception of space in Paul Celan's poetics, comparing it to Martin Buber's and developing a notion of 'realisation', important to both Celan and Buber. Partant du concept du fantastique en tant qu'espace dans laquelle les phénomènes sont véritablement perçus au lieu de simplement se dérouler, l'article montre comment la rupture avec la réalité accoutumée peut mener à une sensation intense de l'être. Chez Martin Buber se trouve la description d'un telle espace, où l'unité est créée à partir de la polarité de tout ce qui est. Le poème peut représenter un exemple d'un tel espace « réalisant ». La conception de l'espace chez Buber est démontrée en dialogue avec le poème STEHEN de Paul Celan, afin de montrer comment le monde réifié est « réalisé » par la poésie. Ainsi sont mis en valeur le rapport mutuel et le lien indispensable entre réalités sociales et la réalité du non-espace.

Evaluating Train Protection Systems

This paper arose from the work carried out for the Cullen/Uff Joint Inquiry into Train Protection Systems. It is concerned with the problem of evaluating the benefits of safety enhancements in order to avoid rare, but catastrophic accidents, and the role of Operations Research in the process. The problems include both input values and representation of outcomes. A key input is the value of life. This paper briefly discusses why the value of life might vary from incident to incident and reviews alternative estimates before producing a 'best estimate' for rail. When the occurrence of an event is uncertain, the normal method is to apply a single 'expected' value. This paper argues that a more effective method of representing such situations is through Monte-Carlo simulation and demonstrates the use of the methodology on a case study of the decision as to whether or not advanced train protection (ATP) should have been installed on a route to the west of London. This paper suggests that the output is more informative than traditional cost-benefit appraisals or engineering event tree approaches. It also shows that, unlike the results from utilizing the traditional approach, the value of ATP on this route would be positive over 50% of the time.

Flexible paleoclimate age-depth models using an autoregressive gamma process

Radiocarbon dating is routinely used in paleoecology to build chronolo- gies of lake and peat sediments, aiming at inferring a model that would relate the sediment depth with its age. We present a new approach for chronology building (called “Bacon”) that has received enthusiastic attention by paleoecologists. Our methodology is based on controlling core accumulation rates using a gamma autoregressive semiparametric model with an arbitrary number of subdivisions along the sediment. Using prior knowledge about accumulation rates is crucial and informative priors are routinely used. Since many sediment cores are currently analyzed, using different data sets and prior distributions, a robust (adaptive) MCMC is very useful. We use the t-walk (Christen and Fox, 2010), a self adjusting, robust MCMC sampling algorithm, that works acceptably well in many situations. Outliers are also addressed using a recent approach that considers a Student-t model for radiocarbon data. Two examples are presented here, that of a peat core and a core from a lake, and our results are compared with other approaches.

Real-life Social Attention in Children with Autism Spectrum Disorders

Autism is a neuro-developmental disorder defined by atypical social behaviour, of which atypical social attention behaviours are among the earliest clinical markers (Volkmar et al., 1997). Eye tracking studies using still images and movie clips have provided a method for the precise quantification of atypical social attention in ASD. This is generally characterised by diminished viewing of the most socially pertinent regions (eyes), and increased viewing of less socially informative regions (body, background, objects) (Klin et al., 2002; Riby & Hancock, 2008, 2009). Ecological validity within eye tracking studies has become an increasingly important issue. As of yet, however, little is known about the precise nature of the atypicalities of social attention in ASD in real-life. Objectives: To capture and quantify gaze patterns for children with an ASD within a real life setting, compared to two Typically Developing (TD) comparison groups. Methods: Nine children with an ASD were compared to two age matched TD groups – a verbal (N=9) and a non-verbal (N=9) comparison group. A real-life scenario was created involving an experimenter posing as a magician, and consisted of 3 segments: a conversation segment; a magic trick segment; and a puppet segment. The first segment explored children’s attentional preferences during a real-life conversation; the magic trick segment explored children’s use of the eyes as a communicative cue, and the puppet segment explored attention capture. Finally, part of the puppet section explored children’s use of facial information in response to an unexpected event. Results: The most striking difference between the groups was the diminished viewing of the eyes by the ASD group in comparison to both control groups. This was found particularly during the conversation segment, but also during the magic trick segment, and during the puppet segment. When in conversation, participants with ASD were found to spend a greater proportion time looking off-screen, in comparison to TD participants. There was also a tendency for the ASD group to spend a greater proportion of time looking to the mouth of the experimenter. During the magic trick segment, despite the fact that the eyes were not predictive of a correct location, both TD comparison groups continued to use the eyes as a communicative cue, whereas the ASD group did not. In the puppet segment, all three groups spent a similar amount of time looking between the puppet and regions of the experimenter’s face. However, in response to an unexpected event, the ASD group were significantly slower to fixate back on the experimenter’s face. Conclusions: The results demonstrate the reduced salience of socially pertinent information for children with ASD in real life, and they provide support for the findings from previous eye tracking studies involving scene viewing. However, the results also highlight a pattern looking off-screen for both the TD and ASD groups. This eye movement behaviour is likely to be associated specifically with real-life interaction, as it has functional relevance (Doherty-Sneddon et al., 2002). However, the fact that it is significantly increased in the ASD group has implications for their understanding of real life social interactions.

Exploring Scale Effects of Best/Worst Rank Ordered Choice Data to Estimate Benefits of Tourism in Alpine Grazing Commons

In many environmental valuation applications standard sample sizes for choice modelling surveys are impractical to achieve. One can improve data quality using more in-depth surveys administered to fewer respondents. We report on a study using high quality rank-ordered data elicited with the best-worst approach. The resulting "exploded logit" choice model, estimated on 64 responses per person, was used to study the willingness to pay for external benefits by visitors for policies which maintain the cultural heritage of alpine grazing commons. We find evidence supporting this approach and reasonable estimates of mean WTP, which appear theoretically valid and policy informative. © The Author (2011).

Association analysis of proopiomelanocortin (POMC) haplotypes in type 1 diabetes in a UK population

Aim

To assess the association of POMC haplotype-tagged single nucleotide polymorphisms (htSNPs) with the development of type 1 diabetes (T1D) in a Caucasian population.

Methods

All exons, intron 1, and approximately 6-kb upstream and 3-kb downstream of the POMC gene were bidirectionally resequenced to identify DNA polymorphisms in 30 individuals. Allele frequencies were determined (60 chromosomes) and efficient htSNPs were selected using the htSNP2 programme. Genotyping was performed in 390 cases, 339 controls and 245 T1D parent-offspring trios, using Taqman, Sequenom and direct-sequencing technologies.

Results

Thirteen polymorphisms (two novel) with a minor allele frequency greater than 1% were identified. Six POMC htSNPs (rs3754863 G>A, ss161151662 A>G, rs3754860 C>T, rs1009388 G>C, rs3769671 A>C, rs1042571 G>A) were identified. Allele and haplotype frequencies were similar between case and control groups (P>0.60 by permutation test), and assessment of allele transmission distortion from informative parents to affected offspring also failed to find any association. Stratification of these analyses for age-at-onset and HLA-DR risk group (DR3/DR4) revealed no significant associations. A haplotype block of 9.86-kb from rs3754863 to rs1042571 was identified, encompassing the POMC gene. Comparison of haplotype frequencies identified the GGCGAG haplotype as protective against T1D in 12.9% of cases vs. 18.3% of controls: ?2=8.18, Pc=0.03 by permutation test.

Conclusion

The POMC SNP haplotype GGCGAG may have a protective effect against T1D in the UK population. However, this finding needs to be replicated, and the cellular and molecular processes influenced by this POMC haplotype determined to fully appreciate its impact.

Genomewide linkage scan of schizophrenia in a large multicenter pedigree sample using single nucleotide polymorphisms

A genomewide linkage scan was carried out in eight clinical samples of informative schizophrenia families. After all quality control checks, the analysis of 707 European-ancestry families included 1615 affected and 1602 unaffected genotyped individuals, and the analysis of all 807 families included 1900 affected and 1839 unaffected individuals. Multipoint linkage analysis with correction for marker-marker linkage disequilibrium was carried out with 5861 single nucleotide polymorphisms (SNPs; Illumina version 4.0 linkage map). Suggestive evidence for linkage ( European families) was observed on chromosomes 8p21, 8q24.1, 9q34 and 12q24.1 in nonparametric and/or parametric analyses. In a logistic regression allele-sharing analysis of linkage allowing for intersite heterogeneity, genomewide significant evidence for linkage was observed on chromosome 10p12. Significant heterogeneity was also observed on chromosome 22q11.1. Evidence for linkage across family sets and analyses was most consistent on chromosome 8p21, with a one-LOD support interval that does not include the candidate gene NRG1, suggesting that one or more other susceptibility loci might exist in the region. In this era of genomewide association and deep resequencing studies, consensus linkage regions deserve continued attention, given that linkage signals can be produced by many types of genomic variation, including any combination of multiple common or rare SNPs or copy number variants in a region. Molecular Psychiatry (2009) 14, 786-795; doi:10.1038/mp.2009.11; published online 17 February 2009

Recurrence of Urothelial Carcinoma of the Bladder: A Role for Insulin-Like Growth Factor-II Loss of Imprinting and Cytoplasmic E-Cadherin Immunolocalization

Purpose:This study documents the frequency of insulin-like growth factor-II (IGF-II) loss of imprinting (LOI) in a series of 87 bladder tissues. E-cadherin (CDH1) immunolocalization was also investigated due to the known redistribution of this adherence protein to the cytoplasm following exogenous exposure to IGF-II.
Experimental Design: Informative IGF-II cases were identified following DNA-PCR amplification and subsequent sequencing of the transcribable ApaI RFLP in exon 9 of IGF-II. Similar approaches using primer-specific cDNA templates identified the imprinting status of IGF-II in these informative cases. CDH1cellular localization was assessed on a tissue microarray platform of 114 urothelial carcinoma of the bladder (UCB) cases (70 pTanoninvasive and 44 pT1laminapropria invasive) using the commercially available Novocastra antibody.
Results: IGF-IILOI was evident in 7 of17 (41%) UCB tumors and 4 of11 (36%) tumor-associated normal urothelial samples.Two of four pT1grade 3 tumors, the subject of much debate concerning their suitability for radical cystectomy, showed LOI at the IGF-II locus. In those tumors showing IGF-II LOI, 4 of 7 (57%) displayed concomitant CDH1cytoplasmic staining. In contrast, only 3 of 10 (30%) IGF-IImaintenance ofimprinting tumorshad concomitant CDH1cytoplasmiclocalization. UCB cell lines displaying cytoplasmic CDH1immunolocalization expressed significantly higher levels of IGF-II (CAL29, HT1376, and RT112) compared with RT4, a cell line displaying crisp membranous CDH1staining. Finally, cytoplasmic CDH1staining was an independent predictor of a shorter time to recurrence independent of tumor grade and stage.
Conclusions: We suggest that CDH1 cytoplasmic immunolocalization as a result of increased IGF-II levels identifies those nonmuscle invasive presentations most likely to recur and therefore might benefit from more radical nonconserving bladder surgery